add new sample_fastqs method to seqeunce_index datasource
start_over() now deletes stepoutputfiles before submissions, to avoid possible race condition
cope with having the same subs as a withdrawn element; update stepoutputfiles of stepstates that have the same subs as a stepstate that just changed its own sofs
most of start_over() put inside a transaction to avoid partially started over states
update() now occurs within a transaction, to give us multiple retries in the case of Lock timeouts
new_requirements() fixed so that time overrides from the use specified in hours instead of seconds work
gave the setups unique names for clarity
no longer requires a runner in --debug mode
added more debug() calls
spacial filter .filt files now defined as type "any", to avoid issues with them looking like txt or binary files depending on phase of moon
basic verifyBAMID pipeline
basic verifyBAMID pipeline
submission handling mode when debugging can take a submission id directly so requirements and something in the submissionqueue no longer required just to test running something
given sub in debug mode now implemented in a way that works
test vcfs are zipped
test vcfs are zipped
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
Str now a synnoym for Text for allowed column types; fixed all searches (including those that happen on a create()) so that DateTimes are deflated
split throw() out into new stack_trace() method
added a throw if not alive during job state finalisation